A microfluidic immunoassay is successfully developed for rapid analysis of cotinine saliva samples, which is a metabolite of nicotine and is widely used as a biomarker to evaluate the smoking status and exposure to tobacco smoke. The core microfluidic chip is fabricated by polydimethylsiloxane (PDMS) with standard soft lithography. Each chip is capable of eight parallel analyses of cotinine samples. The analyses can be completed within 40 min with 12 μl sample consumption. The linear detection range is 1 ~ 250 ng/ml and the minimum detectable concentration is 1 ng/ml respectively. The correlation coefficient of the calibration curve established from standard samples is 0.9989. The immunoassay was also validated by real saliva samples, and the results showed good reproducibility and accuracy. All the results were confirmed with traditional ELISA measurements. The result from microfluidic chip device and ELISA kits showed good correspondence, and the correlation coefficients are higher than 0.99. Compared with traditional technique, this microfluidic immunoassay is more economic, rapid, simple and sensitive, perfect for on-site cotinine measurements as well as for the evaluation of the exposure to tobacco smoking. Moreover, this immunoassay has potential to be applied in the analysis of other biomarkers in human saliva samples.